this is embarrassing: rename again to mappy
This commit is contained in:
Heng Li
parent
eaaf53c9b8
commit
d5012a1b17
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@ -4,8 +4,8 @@ include ksw2_dispatch.c
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include getopt.c
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include main.c
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include README.md
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include python/mmappy.c
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include python/cmmappy.h
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include python/cmmappy.pxd
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include python/mmappy.pyx
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include python/mappy.c
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include python/cmappy.h
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include python/cmappy.pxd
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include python/mappy.pyx
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include python/README.rst
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2
Makefile
2
Makefile
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@ -56,7 +56,7 @@ ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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clean:
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rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mmappy.so mmappy.c python/mmappy.c mmappy.egg*
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rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg*
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depend:
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(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
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@ -1,15 +1,15 @@
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===============================
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Mmappy: Minimap2 Python Binding
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===============================
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==============================
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Mappy: Minimap2 Python Binding
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==============================
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`Minimap2 <https://github.com/lh3/minimap2>`_ is a fast and accurate pairwise
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aligner for genomic and transcribed nucleotide sequences. This module wraps
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minimap2 and provides a convenient interface to calling minimap2 in Python.
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aligner for genomic and transcribed nucleotide sequences. This Python extension
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provides a convenient interface to calling minimap2 in Python.
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Installation
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------------
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The mmappy module can be installed directly with:
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The mappy module can be installed directly with:
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.. code:: shell
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@ -21,7 +21,7 @@ or with `pip <https://en.wikipedia.org/wiki/Pip_(package_manager)>`_:
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.. code:: shell
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pip install --user mmappy
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pip install --user mappy
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Usage
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-----
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@ -30,8 +30,8 @@ The following Python program shows the key functionality of this module:
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.. code:: python
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import mmappy as mm
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a = mm.Aligner("test/MT-human.fa") # load or build index
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import mappy as mp
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a = mp.Aligner("test/MT-human.fa") # load or build index
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if not a: raise Exception("ERROR: failed to load/build index")
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for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
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print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
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@ -43,7 +43,7 @@ and prints them out.
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APIs
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----
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Class mmappy.Aligner
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Class mappy.Aligner
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~~~~~~~~~~~~~~~~~~~~~~
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.. code:: python
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@ -86,7 +86,7 @@ Arguments:
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This method maps :code:`seq` against the index. It *yields* a generator,
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generating a series of :code:`Alignment` objects.
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Class mmappy.Alignment
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Class mappy.Alignment
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~~~~~~~~~~~~~~~~~~~~~~~~
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This class has the following properties:
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@ -1,5 +1,5 @@
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#ifndef CMMAPPY_H
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#define CMMAPPY_H
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#ifndef CMAPPY_H
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#define CMAPPY_H
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#include <stdlib.h>
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#include "minimap.h"
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@ -62,7 +62,7 @@ cdef extern from "minimap.h":
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void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
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#
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# Mapping (key struct defined in cmmappy.h below)
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# Mapping (key struct defined in cmappy.h below)
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#
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ctypedef struct mm_reg1_t:
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pass
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@ -77,7 +77,7 @@ cdef extern from "minimap.h":
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#
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# Helper header (because it is hard to expose mm_reg1_t with Cython
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#
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cdef extern from "cmmappy.h":
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cdef extern from "cmappy.h":
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ctypedef struct mm_hitpy_t:
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const char *ctg
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int32_t ctg_start, ctg_end
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@ -1,6 +1,6 @@
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from libc.stdint cimport uint8_t, int8_t
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from libc.stdlib cimport free
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cimport cmmappy
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cimport cmappy
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cdef class Alignment:
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cdef int _ctg_len, _r_st, _r_en
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@ -69,23 +69,23 @@ cdef class Alignment:
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str(self._blen - self._NM), str(self._blen), str(self._mapq), "NM:i:" + str(self._NM), tp, "cg:Z:" + self.cigar_str])
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cdef class ThreadBuffer:
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cdef cmmappy.mm_tbuf_t *_b
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cdef cmappy.mm_tbuf_t *_b
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def __cinit__(self):
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self._b = cmmappy.mm_tbuf_init()
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self._b = cmappy.mm_tbuf_init()
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def __dealloc__(self):
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cmmappy.mm_tbuf_destroy(self._b)
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cmappy.mm_tbuf_destroy(self._b)
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cdef class Aligner:
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cdef cmmappy.mm_idx_t *_idx
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cdef cmmappy.mm_idxopt_t idx_opt
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cdef cmmappy.mm_mapopt_t map_opt
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cdef cmappy.mm_idx_t *_idx
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cdef cmappy.mm_idxopt_t idx_opt
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cdef cmappy.mm_mapopt_t map_opt
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def __cinit__(self, fn_idx_in, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, best_n=None, n_threads=3, fn_idx_out=None):
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cmmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
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cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
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if preset is not None:
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cmmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset
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cmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset
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self.map_opt.flag |= 4 # always perform alignment
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self.idx_opt.batch_size = 0x7fffffffffffffffL # always build a uni-part index
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if k is not None: self.idx_opt.k = k
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@ -96,40 +96,40 @@ cdef class Aligner:
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if bw is not None: self.map_opt.bw = bw
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if best_n is not None: self.best_n = best_n
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cdef cmmappy.mm_idx_reader_t *r;
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cdef cmappy.mm_idx_reader_t *r;
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if fn_idx_out is None:
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r = cmmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, NULL)
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r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, NULL)
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else:
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r = cmmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, fn_idx_out)
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r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, fn_idx_out)
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if r is not NULL:
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self._idx = cmmappy.mm_idx_reader_read(r, n_threads) # NB: ONLY read the first part
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cmmappy.mm_idx_reader_close(r)
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cmmappy.mm_mapopt_update(&self.map_opt, self._idx)
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self._idx = cmappy.mm_idx_reader_read(r, n_threads) # NB: ONLY read the first part
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cmappy.mm_idx_reader_close(r)
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cmappy.mm_mapopt_update(&self.map_opt, self._idx)
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def __dealloc__(self):
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if self._idx is not NULL:
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cmmappy.mm_idx_destroy(self._idx)
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cmappy.mm_idx_destroy(self._idx)
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def __bool__(self):
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return (self._idx != NULL)
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def map(self, seq, buf=None):
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cdef cmmappy.mm_reg1_t *regs
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cdef cmmappy.mm_hitpy_t h
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cdef cmappy.mm_reg1_t *regs
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cdef cmappy.mm_hitpy_t h
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cdef ThreadBuffer b
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cdef int n_regs
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if self._idx is NULL: return None
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if buf is None: b = ThreadBuffer()
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else: b = buf
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regs = cmmappy.mm_map(self._idx, len(seq), str.encode(seq), &n_regs, b._b, &self.map_opt, NULL)
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regs = cmappy.mm_map(self._idx, len(seq), str.encode(seq), &n_regs, b._b, &self.map_opt, NULL)
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for i in range(n_regs):
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cmmappy.mm_reg2hitpy(self._idx, ®s[i], &h)
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cmappy.mm_reg2hitpy(self._idx, ®s[i], &h)
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cigar = []
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for k in range(h.n_cigar32):
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c = h.cigar32[k]
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cigar.append([c>>4, c&0xf])
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yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.blen, h.NM, h.trans_strand)
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cmmappy.mm_free_reg1(®s[i])
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cmappy.mm_free_reg1(®s[i])
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free(regs)
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@ -1,7 +1,7 @@
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#!/usr/bin/env python
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import sys, getopt
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import mmappy as mm
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import mappy as mp
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def readfq(fp): # multi-line fasta/fastq parser
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last = None
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@ -39,7 +39,7 @@ def main(argv):
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if len(args) < 2:
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print("Usage: mm2-lite.py <ref.fa>|<ref.mmi> <query.fq>")
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sys.exit(1)
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a = mm.Aligner(args[0]) # load/build index
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a = mp.Aligner(args[0]) # load/build index
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if not a:
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print("ERROR: failed to load/build index")
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return
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10
setup.py
10
setup.py
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@ -9,9 +9,9 @@ cmdclass = {}
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try:
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from Cython.Build import build_ext
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except ImportError: # without Cython
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module_src = 'python/mmappy.c'
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module_src = 'python/mappy.c'
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else: # with Cython
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module_src = 'python/mmappy.pyx'
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module_src = 'python/mappy.pyx'
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cmdclass['build_ext'] = build_ext
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import sys
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@ -22,7 +22,7 @@ def readme():
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return f.read()
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setup(
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name = 'mmappy',
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name = 'mappy',
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version = '2.2rc2',
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url = 'https://github.com/lh3/minimap2',
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description = 'Minimap2 python binding',
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@ -31,13 +31,13 @@ setup(
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author_email = 'lh3@me.com',
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license = 'MIT',
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keywords = ['bioinformatics', 'sequence-alignment'],
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ext_modules = [Extension('mmappy',
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ext_modules = [Extension('mappy',
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sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c',
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'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
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'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c'],
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depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
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'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
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'python/cmmappy.h', 'python/cmmappy.pxd'],
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'python/cmappy.h', 'python/cmappy.pxd'],
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extra_compile_args = ['-msse4'], # WARNING: ancient x86_64 CPUs don't have SSE4
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include_dirs = ['.'],
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libraries = ['z', 'm', 'pthread'])],
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